2IZ9

MS2-RNA HAIRPIN (4ONE -5) COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Deletion of a Single Hydrogen Bonding Atom from the MS2 RNA Operator Leads to Dramatic Rearrangements at the RNA-Coat Protein Interface

Grahn, E., Stonehouse, N.J., Adams, C.J., Fridborg, K., Beigelman, L., Matulic-Adamic, J., Warriner, S.L., Stockley, P.G., Liljas, L.

(2000) Nucleic Acids Res. 28: 4611


  • PubMed Abstract: 

    • The MS2 coat protein binds specifically to an RNA hairpin formed within the viral genome. By soaking different RNA fragments into crystals of MS2 coat protein capsids it is possible to determine the X-ray structure of the RNA-protein complexes formed ...

    The MS2 coat protein binds specifically to an RNA hairpin formed within the viral genome. By soaking different RNA fragments into crystals of MS2 coat protein capsids it is possible to determine the X-ray structure of the RNA-protein complexes formed. Here we present the structure to 2.85 A resolution of a complex between a chemically modified RNA hairpin variant and the MS2 coat protein. This RNA variant has a substitution at the -5 base position, which has been shown previously to be pyrimidine-specific and is a uracil in the wild-type RNA. The modified RNA hairpin contains a pyridin-4-one base (4one) at this position that lacks the exocyclic 2-oxygen eliminating the possibility of forming a hydrogen bond to asparagine A87 in the protein. The 4one complex structure shows an unprecedented major conformational change in the loop region of the RNA, whereas there is almost no change in the conformation of the protein.

    Organizational Affiliation: 

    Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MS2 COAT PROTEIN
A, B, C
129Escherichia phage MS2Mutation(s): 0 
Find proteins for P03612 (Escherichia phage MS2)
Go to UniProtKB:  P03612
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'R,S19Enterobacteria phage MS2
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ONE
Query on ONE
R, S
RNA LINKINGC10 H14 N O8 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.200 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 288.000α = 90.00
b = 288.000β = 90.00
c = 653.000γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection